Figure 6. Example of finding the correct alignment between remote homologs.

Top: The structural alignment of template DXR (purple) and query KaiA (yellow). Close structural homology clearly exists among the common portion (four structurally equivalent strands and four structurally equivalent helices, loops are not represented for clarity) despite a significant deletion of 4 SSEs in DXR (shown in grey). Bottom: With helices depicted as rectangles and strands as arrows, the top two rows depict the correct correspondence of template and query SSEs based on the structure-based sequence alignment. The next row shows the same correspondence is found in the best alignment in the S4 ensemble. The last line shows the optimal alignment which pairs four SSEs incorrectly.